Deep divergences among inconspicuously colored clades of Epipedobates poison frogs.

Poison frogs (Dendrobatidae) are famous for their aposematic species, having a combination of diverse color patterns and defensive skin toxins, yet most species in this family are inconspicuously colored and considered non-aposematic. Epipedobates is among the youngest genus-level clades of Dendrobatidae that includes both aposematic and inconspicuous species. Using Sanger-sequenced mitochondrial and nuclear markers, we demonstrate deep genetic divergences among inconspicuous species of Epipedobates but relatively shallow genetic divergences among conspicuous species. Our phylogenetic analysis includes broad geographic sampling of the inconspicuous lineages typically identified as E. boulengeri and E. espinosai, which reveals two putative new species, one in west-central Colombia (E. sp. 1) and the other in north-central Ecuador (E. aff. espinosai). We conclude that E. darwinwallacei is a junior subjective synonym of E. espinosai. We also clarify the geographic distributions of inconspicuous Epipedobates species including the widespread E. boulengeri. We provide a qualitative assessment of the phenotypic diversity in each nominal species, with a focus on the color and pattern of inconspicuous species. We conclude that Epipedobates contains eight known valid species, six of which are inconspicuous. A relaxed molecular clock analysis suggests that the most recent common ancestor of Epipedobates is âˆ¼11.1 million years old, which nearly doubles previous estimates. Last, genetic information points to a center of species diversity in the Chocó at the southwestern border of Colombia with Ecuador. A Spanish translation of this text is available in the supplementary materials.

Chromosomal Inversions and the Demography of Speciation in Drosophila montana and Drosophila flavomontana.

Chromosomal inversions may play a central role in speciation given their ability to locally reduce recombination and therefore genetic exchange between diverging populations. We analyzed long- and short-read whole-genome data from sympatric and allopatric populations of 2 Drosophila virilis group species, Drosophila montana and Drosophila flavomontana, to understand if inversions have contributed to their divergence. We identified 3 large alternatively fixed inversions on the X chromosome and one on each of the autosomes 4 and 5. A comparison of demographic models estimated for inverted and noninverted (colinear) chromosomal regions suggests that these inversions arose before the time of the species split. We detected a low rate of interspecific gene flow (introgression) from D. montana to D. flavomontana, which was further reduced inside inversions and was lower in allopatric than in sympatric populations. Together, these results suggest that the inversions were already present in the common ancestral population and that gene exchange between the sister taxa was reduced within inversions both before and after the onset of species divergence. Such ancestrally polymorphic inversions may foster speciation by allowing the accumulation of genetic divergence in loci involved in adaptation and reproductive isolation inside inversions early in the speciation process, while gene exchange at colinear regions continues until the evolving reproductive barriers complete speciation. The overlapping X inversions are particularly good candidates for driving the speciation process of D. montana and D. flavomontana, since they harbor strong genetic incompatibilities that were detected in a recent study of experimental introgression.

Comparative genomics of the Neodiprion sertifer nucleopolyhedrovirus from Turkey with the fewest ORFs among baculoviruses.

The complete genome of a European pine sawfly Neodiprion sertifer nucleopolyhedrovirus (NeseNPV-TR) was sequenced and characterized from next-generation sequencing data of N. sertifer larva from Türkiye. This genome was analyzed and compared to previously reported genomes of baculoviruses. The baculovirus phylogeny was reconstructed and the species identity of the NeseNPV-TR was delineated using K2P distance. The length of the genome was 82,052 bp, with a G + C content of 33.28%. It contained 83 putative ORFs, including 38 baculovirus core genes, three lepidopteran baculovirus core genes, and three non-conserved genes. It had five hrs with 20.6% overall mean distance on average. The pairwise K2P distances of lef-8, lef-9, and polh genes and combinations of three genes and 38 genes between NeseNPV-TR and NeseNPV were slightly higher than the specified threshold values for species demarcation. The most variable genes were lef-2, helicase, p40, desmoplakin, pif7, p6.9, vp91, and vp39, while the most conserved were lef-8, lef-9, odv-e18, pif2, and lef-5 among baculoviruses. The genome of NeseNPV-TR is smaller and contains the fewest ORFs among baculoviruses. Some of unassigned ORFs had conserved domains and hence, we suggest further investigation to determine their structural and functional roles. Phylogenetic analyses confirmed its position within genus Gammabaculovirus. Taking into account the phylogenetic position, K2P distances, and NJ tree, the NeseNPV-TR can be classified in the same species (Gammabaculovirus nesertiferis) with NeseNPV. The different divergence rates in the baculovirus core genes may be related with different selection pressures acting on the genes. The lower genetic diversity of Group I alphabaculoviruses is most probably due to recent emergence.

Epigenetic and Genetic Differentiation Between Coregonus Species Pairs.

Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental conditions for many generations, though there has been minimal empirical research on epigenetically induced mutagenesis in diversification and speciation. Whitefish, freshwater members of the salmonid family, are excellent systems to study phenotypic diversification and speciation due to the repeated divergence of benthic-limnetic species pairs serving as natural replicates. Here we investigate whole genome genetic and epigenetic differentiation between sympatric benthic-limnetic species pairs in lake and European whitefish (Coregonus clupeaformis and Coregonus lavaretus) from four lakes (N = 64). We found considerable, albeit variable, genetic and epigenetic differences between species pairs. All SNP types were enriched at CpG sites supporting the mutagenic nature of DNA methylation, though C>T SNPs were most common. We also found an enrichment of overlaps between outlier SNPs with the 5% highest FST between species and differentially methylated loci. This could possibly represent differentially methylated sites that have caused divergent genetic mutations between species, or divergent selection leading to both genetic and epigenetic variation at these sites. Our results support the hypothesis that DNA methylation contributes to phenotypic divergence and mutagenesis during whitefish speciation.

Prevalence and phylogenetic analysis of Gyrovirus galga 1 in southern China from 2020 to 2022.

Since 2011, the Gyrovirus galga 1 (GyVg1, previously recognized as avian gyrovirus 2) strain has extensively been detected worldwide. However, because there are no up-to-date reports of examining the distribution of GyVg1 in flocks in southern China, the epidemiology of this virus is unknown. To investigate the prevalence and genetic evolution of GyVg1, a total of 2,077 field samples collected from 113 chicken farms in 6 provinces in southern China during 2020 to 2022 were tested. Among them, 315 samples (315/2,077, 15.17%) were positive for GyVg1 by PCR. The positive rate of GyVg1 detection between different regions of southern China ranged from 11.69% (Guangdong) to 22.46% (Yunnan). The correlation between GyVg1 prevalence and sample source groups was analyzed, the results showing that the highest seroprevalence of GyVg1 was observed in visceral tissues (27.34%, 187/684), significantly higher (P < 0.05) than that of feather shafts (17.22%, 31/180), serums (8.85%, 78/881), and fecal (5.72%, 19/332). Additionally, the complete genomes of 10 GyVg1 strains were sequenced and analyzed, which showed nucleotide identities of 96.2 to 99.9%, 97.0 to 100.0%, 95.2 to 100.0%, and 95.7 to 99.8% in the complete genome, ORF1, ORF2, and ORF3, respectively, and 94.4 to 100.0%, 91.3 to 100.0%, and 98.7 to 100.0% amino acid similarity in the VP2, VP3, and VP1 proteins, respectively. Phylogenetic analysis of the whole genome showed that 10 GyVg1 strains belong to genotype I, and one strain belongs to genotype III. Sequence analysis showed several amino acid substitutions in both the VP1, VP2, and VP3 proteins. Our results enhance the understanding of the molecular characterization of GyVg1 infection in southern China. In conclusion, this study reveals the high prevalence and high genetic differentiation of GyVg1 in Chinese chickens and suggests that the potential impact of GyVg1 on the chicken industry may be of concern.

Genomic divergence and demographic history of Quercus aliena populations.

BACKGROUND: Quercus aliena is a major montane tree species of subtropical and temperate forests in China, with important ecological and economic value. In order to reveal the species' population dynamics, genetic diversity, genetic structure, and association with mountain habitats during the evolutionary process, we re-sequenced the genomes of 72 Q. aliena individuals. RESULTS: The whole chloroplast and nuclear genomes were used for this study. Phylogenetic analysis using the chloroplast genome dataset supported four clades of Q. aliena, while the nuclear dataset supported three major clades. Sex-biased dispersal had a critical role in causing discordance between the chloroplast and nuclear genomes. Population structure analysis showed two groups in Q. aliena. The effective population size sharply declined 1 Mya, coinciding with the Poyang Glaciation in Eastern China. Using genotype-climate association analyses, we found a positive correlation between allele frequency variation in SNPs and temperature, suggesting the species has the capacity to adapt to changing temperatures. CONCLUSION: Overall, this study illustrates the genetic divergence, genomic variation, and evolutionary processes behind the demographic history of Q. aliena.

Integrated Identification and Genetic Diversity of Potentially Invasive Clearwing Moths (Lepidoptera: Cossoidea: Sesiidae) in Korea.

The populations of clearwing moth borers in Korea have recently caused extensive and severe damage to pin oaks (Quercus palustris Munchh.). We conducted field monitoring and molecular analyses to identify them in an integrated manner. Morphological examination and molecular analyses of the COI gene, based on intra- and interspecific genetic divergences (GDs), revealed that the borers were identified as two invasive species, Sphecodoptera sheni and Paranthrenella pinoakula sp. nov. The maximum intraspecific GD was found to be 1.9%, whereas the minimum interspecific GD was confirmed as 8.1%, indicating a distinct barcoding gap. Both the MJ network and NJ tree also showed that 18 haplotypes (Hs) were detected from the 52 COI sequences. The borers revealed a total of 17 Hs: (i) H1-H7 were detected in all seven regions with S. sheni; (ii) Wonju and Goyang populations of S. sheni revealed more than three Hs; (iii) H7 was closely connected with H8 of the Chinese population of S. sheni; (iv) H9-H10 were detected in other samples from the Wonju population with P. pinoakula sp. n. and were closely located with congeneric species. A maximum likelihood tree also revealed that P. pinoacula sp. n. nested within the congeneric species, genetically separating from S. sheni.

Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4+ T cells.

HIV can persist in a latent form as integrated DNA (provirus) in resting CD4+ T cells of infected individuals and as such is unaffected by antiretroviral therapy (ART). Despite being a major obstacle for eradication efforts, the genetic variation and timing of formation of this latent reservoir remains poorly understood. Previous studies on when virus is deposited in the latent reservoir have come to contradictory conclusions. To reexamine the genetic variation of HIV in CD4+ T cells during ART, we determined the divergence in envelope sequences collected from 10 SIV infected rhesus macaques. We found that the macaques displayed a biphasic decline of the viral divergence over time, where the first phase lasted for an average of 11.6 weeks (range 4-28 weeks). Motivated by recent observations that the HIV-infected CD4+ T cell population is composed of short- and long-lived subsets, we developed a model to study the divergence dynamics. We found that SIV in short-lived cells was on average more diverged, while long-lived cells harbored less diverged virus. This suggests that the long-lived cells harbor virus deposited starting earlier in infection and continuing throughout infection, while short-lived cells predominantly harbor more recent virus. As these cell populations decayed, the overall proviral divergence decline matched that observed in the empirical data. This model explains previous seemingly contradictory results on the timing of virus deposition into the latent reservoir, and should provide guidance for future eradication efforts.

Genetic divergences and hybridization within the Sebastes inermis complex.

The Sebastes inermis complex includes three sympatric species (Sebastes cheni, viz Sebastes inermis, and Sebastes ventricosus) with clear ecomorphological differences, albeit incomplete reproductive isolation. The presence of putative morphological hybrids (PMH) with plausibly higher fitness than the parent species indicates the need to confirm whether hybridization occurs within the complex. In this sense, we assessed the dynamics of genetic divergence and hybridization within the species complex using a panel of 10 microsatellite loci, and sequences of the mitochondrial control region (D-loop) and the intron-free rhodopsin (RH1) gene. The analyses revealed the presence of three distinct genetic clusters, large genetic distances using D-loop sequences, and distinctive mutations within the RH1 gene. These results are consistent with the descriptions of the three species. Two microsatellite loci had signatures of divergent selection, indicating that they are linked to genomic regions that are crucial for speciation. Furthermore, nonsynonymous mutations within the RH1 gene detected in S. cheni and "Kumano" (a PMH) suggest dissimilar adaptations related to visual perception in dim-light environments. The presence of individuals with admixed ancestry between two species confirmed hybridization. The presence of nonsynonymous mutations within the RH1 gene and the admixed ancestry of the "Kumano" morphotype highlight the potential role of hybridization in generating novelties within the species complex. We discuss possible outcomes of hybridization within the species complex, considering hybrid fitness and assortative mating. Overall, our findings indicate that the genetic divergence of each species is maintained in the presence of hybridization, as expected in a scenario of speciation-with-gene-flow.

Comparative Mitogenomics Reveals Cryptic Species in Sillago ingenuua McKay, 1985 (Perciformes: Sillaginidae).

It is unreliable to identify marine fishes only by external morphological features. Species misidentification brings great challenges to fishery research, resource monitoring and ecomanagement. Sillago ingenuua is an important part of commercial marine fishes, and in which, the morphological differences between different groups are not obvious. Here, we compared different geographical groups of S. ingenuua which were collected from Xiamen, Dongshan, Keelung, Songkhla and Java. The results showed that all samples of S. ingenuua were similar in external morphological characteristics and the shape of the swim bladder, but there were two distinctive lineages which were flagged as cryptic species based on DNA barcoding. The comparative mitogenomic results showed that S. ingenuua A and S. ingenuua B were identical in structural organization and gene arrangement. Their nucleotide composition and codon usage were also similar. A phylogenetic analysis was performed based on 13 concatenated PCGs from eight Sillago species. The results showed that the genetic distance between S. ingenuua A and S. ingenuua B was large (D = 0.069), and this genetic distance was large enough to reveal that S. ingenuua A and S. ingenuua B might be different species.

Integrative taxonomic analyses reveal first country records of Occidozygashiwandashanensis Chen, Peng, Liu, Huang, Liao & Mo, 2022 and Hylaranalatouchii (Boulenger, 1899) (Anura, Dicroglossidae, Ranidae) from Vietnam.

Background: Occidozygashiwandashaensis was recently discovered from Guangxi Province of China. Hylaranalatouchii is a widespread species in southern China, including Hong Kong and Taiwan. Both species are expected to be found in the border areas between Vietnam and China; however, no records of these frogs have been documented from Vietnam so far. New information: We record two species of amphibians for the first time from Vietnam, namely Occidozygashiwandashaensis from Bac Giang Province and Hylaranalatouchii from Hai Phong City and Quang Ninh Province in northern Vietnam. Morphologically, the Vietnamese representatives of O.shiwandashanensis resemble the type series from China. The specimens of H.latouchii from Vietnam slightly differ from the type series from China by having a larger size (SVL 48.6-51.7 mm in males, SVL 58.4 mm in the females vs. 36.0-40.0 mm in males, 42.0-53.0 mm in females). Genetic distances between the Vietnamese records and the type specimens of O.shiwandashanensis from China varied from 0 to 1.5% (16S gene). Genetic divergences between the Vietnamese records and H.latouchii from the type locality were 2.0-2.6% (16S gene). In addition, morphological data and natural history notes of the aforementioned species are provided, based on the new records from Vietnam. -.

Divergence in the internal genital morphology of females and correlated divergence in male intromittent structures among populations of a millipede.

Our understanding of genital evolution comes largely from studies of male genitalia. Females have received far less attention because of the difficulties inherent in quantifying the shapes of their internal genital structures. Here we combine advances in micro-computed tomography with a new landmark free method of quantifying three-dimensional trait shape, to document patterns of divergence in female genital shape, and the correlated divergence of male genitalia among populations of the millipede Antichiropus variabilis. We used single-nucleotide polymorphisms to estimate levels of neutral genetic divergence among seven populations of millipede. Genetic divergence was high and correlated with geographic distance. Comparing phenotypic divergence in genital shape to neutral genetic divergence, we found that genital shape for both females and males has diverged more than would be expected from random drift, consistent with a pattern of directional selection. While there was significant covariation between female and male genital shape across populations, the magnitude of divergence in genital shape between the sexes was not correlated. Our results demonstrate the utility of using three-dimensional scanning technologies to examine female genital traits and add to a small but growing number of studies showing that like male genitalia, female genitalia can be under strong directional selection.

Genetic differentiation and species diversification of the Adoxophyes orana complex (Lepidoptera: Tortricidae) in East Asia.

The Adoxophyes tea tortrix (Lepidoptera: Tortricidae) is a group of leaf rollers that cause enormous economic losses on tea and apple crops. In East Asia, taxonomic ambiguity of the Adoxophyes orana complex (AOC), which consists of A. orana, A. dubia, A. honmai, and A. paraorana, has persisted for decades because of vague diagnostic characters. In this study, differences in the AOC were examined to improve species identification, determine genetic variations, and develop control strategies. Analyses revealed that A. orana comprised 2 lineages, a widely distributed Palearctic lineage and an East Asian lineage that was nested with other Asian species. Genetic divergence of >3% is proposed to confirm the AOC species that would benefit subsequent taxonomic revision. The monophyletic Taiwanese A. sp. with 2.8-4% from other AOC species appeared to suggest it as an independent taxon, and low interspecific divergence between A. honmai and A. dubia of 0.3% indicated possibility of recent divergence or intraspecific variations. Our result further suggested that the Z9-14:Ac ratio of semiochemicals could be a reference for the reblending of pheromone attractants in Taiwanese tea plantations. Moreover, the AOC species appeared to have a tendency of specific geographic distributions, with A. dubia and A. honmai in Japan and China, A. paraorana in Korea, and A. sp. in Taiwan. Maintaining the unique genetic composition of Adoxophyes species in each geographic region and preventing the possible invasions into those AOC-free countries through the transportation of host plants are essential in managing the AOC in East Asia.

Morphological and molecular analysis of the tropical hermit crab Calcinus vachoni (Decapoda, Diogenidae) and its potential association with colonial anemone.

Calcinus is the colorful hermit crab genus belonging to the family Diogenidae and is often found in coral reefs of the tropical Indo-West Pacific region, including southern Honshu, Japan, which is the northern limit of their occurrence. In the present study, we found C. vachoni for the first time in the intertidal zone of Jeju Island-the southernmost island of South Korea. We examined their morphology and provided a diagnosis of their morphological details with illustrations. In addition, the Korean Calcinus population was genetically characterized using mtDNA cox1 sequences and by placing them into three previously reported regional haplogroups. The phylogenetic tree from maximum likelihood analysis revealed that Korean C. vachoni is assigned to the C. vachoni haplogroups exclusively, one of the three well-supported mitochondrial haplogroups with distinct geographic ranges (i.e., C. vachoni, C. aff. vachoni Cooks, and C. aff. vachoni Mascarenes). This result provides new information on the species distribution of C.vachoni, extending their geographic range further north into the southern coast of Korea. In this study, we also first report the potential association of C. vachoni with their co-occurring colonial anemone species Palythoa aff. mutuki and dead coral head of Pocillopora species based on our on-site observation and a public coral collection database of Calcinus species. However, their ecological association with co-occurring coral species is putatively assumed for now and therefore has to be validated by compelling evidence from further field observation and experimental studies (i.e., whether the presence/absence of colonial anemones affects the behavior and survival of the hermit crabs).

Phylogeography of 912 Cherry Accessions Insight into Independent Origins of Fruiting Cherries and Domestication Footprints of Cultivated Chinese Cherry (Prunus pseudocerasus Lindl.).

The subgenus Cerasus (Rosaceae) contain numerous fruit trees and ornamentals with high economic values. The origin and genetic divergence among various types of fruiting cherries always remain a perplexing issue. We employed three plastom fragments and ITS sequence matrices derived from 912 cherry accessions to elucidate the phylogeographic structure and genetic relationship among fruiting cherries, as well as the origin and domestication of cultivated Chinese cherry. The integration of haplotype genealogies, Approximate Bayesian computation (ABC) approach and estimation of genetic differentiation within and between different groups and lineages has facilitated the resolution of several previously unresolved questions. Firstly, distant phylogenetic relationships between Cerasus and Microcerasus accessions, as indicated by both nuclear and chloroplast data, suggested independent origins and evolution for these two taxa. Moreover, two distinct geographic origin centers (Europe and China) have been confirmed, with significant phylogeographic signals and high genetic differentiation observed between cherries from these regions. This may be attributed to long-term geographic isolation caused by Himalaya-Hengduan Mountains. Our phylogeographic analyses and ABC analysis suggested that cherries inhabiting in China may have undergone multiple hybridization events during the glacial refugia of the eastern edge and southern Himalaya-Hengduan Mountains, followed by rapid radiation throughout their current habitats during interglacial period. The discrepancy between nuclear and chloroplast data may be attributed to hybridization events and incomplete lineage sorting. Furthermore, we speculated that the domesticated Chinese cherries were derived from wild accessions in Longmenshan Fault Zones approximately 2600 years ago. We have also traced the domestication processes and dispersal routes of cultivated Chinese cherries.

Chromosome-level genome and population genomics provide novel insights into adaptive divergence in allopatric Eleutheronema tetradactylum.

Understanding the adaptive ecological divergence provides important information for revealing biodiversity generation and maintenance. Adaptive ecology divergence in populations occurs in various environments and locations, but its genetic underpinnings remain elusive. We generated a chromosome-level genome of Eleutheronema tetradactylum (~582 Mb) and re-sequenced 50 allopatric E. tetradactylum in two independent environmental axes in China and Thailand Coastal waters as well as 11 cultured relatives. A low level of whole genome-wide diversity explained their decreased adaptive potential in the wild environment. Demographic analysis showed evidence of historically high abundance followed by a continuous distinct decline, plus signs of recent inbreeding and accumulation of deleterious mutations. Extensive signals of selective sweeps with signs of local adaptation to environmental differentiation between China and Thailand at genes related to thermal and salinity adaptation were discovered, which might be the driving factors of the geographical divergence of E. tetradactylum. Many genes and pathways subjected to strong selection under artificial breeding were associated with fatty acids and immunity (ELOVL6L, MAPK, p53/NF-kB), likely contributing to the eventual adaptation of artificial selective breeding. Our comprehensive study provided crucial genetic information for E. tetradactylum, with implications for the further conservation efforts of this threatened and ecologically valuable fish.

Uncovering neglected subtypes and zoonotic transmission of Hepatitis E virus (HEV) in Brazil.

Hepatitis E virus (HEV) circulation in humans and swine has been extensively studied in South America over the last two decades. Nevertheless, only 2.1% of reported HEV strains are available as complete genome sequences. Therefore, many clinical, epidemiological, and evolutionary aspects of circulating HEV in the continent still need to be clarified. Here, we conducted a retrospective evolutionary analysis of one human case and six swine HEV strains previously reported in northeastern, southern, and southeastern Brazil. We obtained two complete and four nearly complete genomic sequences. Evolutionary analysis comparing the whole genomic and capsid gene sequences revealed high genetic variability. This included the circulation of at least one unrecognized unique South American subtype. Our results corroborate that sequencing the whole capsid gene could be used as an alternative for HEV subtype assignment in the absence of complete genomic sequences. Moreover, our results substantiate the evidence for zoonotic transmission by comparing a larger genomic fragment recovered from the sample of the autochthonous human hepatitis E case. Further studies should continuously investigate HEV genetic diversity and zoonotic transmission of HEV in South America.

DNA Barcoding of the Palaearctic Elfin Butterflies (Lepidoptera, Lycaenidae) with a Description of Four New Species from Vietnam.

Phylogenetic analysis is provided for the first time for 12 species of Palaearctic elfin butterflies, members of the previously recognized genera Ahlbergia Bryk, 1947, Cissatsuma Johnson, 1992, and Novosatsuma Johnson, 1992, based on the barcoding region of the mitochondrial cytochrome C oxidase subunit I gene (COI). Comparison of the COI barcodes revealed very low levels of genetic divergence between the species of the Palaearctic elfin butterflies and Callophrys Billberg, 1820 sensu stricto. COI-based phylogeny revealed that Palaearctic Callophrys and the Palaearctic elfin butterflies, except Cissatsuma, are polyphyletic. Four new sympatric species, namely, Callophrys (Ahlbergia) hmong sp. n., C. (A.) tay sp. n., Callophrys (Cissatsuma) devyatkini sp. n. and C. (A.) dao sp. n. are described from Ha Giang Province, North Vietnam, based on wing colouration, the morphologies of the male and female genitalia, and differences in COI sequences. Discovery of the new species expands the distribution range of the group towards the southeast, beyond the Palaearctic region.

Genomic assessment reveals signal of adaptive selection in populations of the Spotted rose snapper Lutjanus guttatus from the Tropical Eastern Pacific.

Background: The lack of barriers in the marine environment has promoted the idea of panmixia in marine organisms. However, oceanographic conditions and habitat characteristics have recently been linked to genetic structure in marine species. The Tropical Eastern Pacific (TEP) is characterized by dynamic current systems and heterogeneous oceanographic conditions. The Gulf of Panama (part of the equatorial segment for the TEP) is influenced by a complex current system and heterogeneous environment, which has been shown to limit the gene flow for shoreline species. Next Generation Sequencing (NGS) has contributed to detect genetic differences in previously reported panmictic species by the assessment of loci associated with selection and to understand how selection acts affects marine populations. Lutjanus guttatus is a species distributed in the TEP for which previous studies using mitochondrial data recovered a panmictic pattern along its distributional range. In this study, we used SNP data of L. guttatus individuals sampled along its range to evaluate population genetic structure and investigate whether oceanographic factors influence the species' genetic architecture. Finally, we assessed the role of adaptive selection by evaluating the contribution of outlier and neutral loci to genetic divergence. Methods: The RADcap method was used to obtain 24 million paired reads for 123 individuals of L. guttatus covering nearly all its distributional area. Genetic variation was assessed using both spatial and non-spatial methods by comparing three different data sets: (i) a Combined Loci (CL dataset = 2003 SNPs); a search for putative loci under selection allowed the evaluation of (ii) Neutral Loci (NL dataset = 1858 SNPs) and (iii) Outlier Loci (OL dataset = 145 SNPs). We used the estimating effective migration surface (EEMS) approach to detect possible barriers to gene flow. Results: Genetic differences were found in the OL dataset, showing two clusters (Northern and Southern), whereas NL showed no differences. This result may be related to the Selection-Migration balance model. The limit between the Northern and Southern groups was in the Gulf of Panama, which has been previously identified as a barrier to gene flow for other species, mainly due to its heterogeneous oceanographic conditions. The results suggest that selection plays an important role in generating genetic differences in Lutjanus guttatus. A migration corridor was detected that coincides with the Costa Rica Coastal Current that flows from Central America to the Gulf of California, allowing the homogenization of the northern population. In the Southern cluster, a migration corridor was observed with the OL from Panama to Colombia, which could be associated with the currents found in the Gulf of Panama. Genetic variation found in the OL of Lutjanus guttatus highlights the usefulness of NGS data in evaluating the role of selection in population differentiation.

Microgeographic variation in early fitness traits of Pinus sylvestris from contrasting soils.

PREMISE: The possibility of fine-scale intraspecific adaptive divergence under gene flow is established by theoretical models and has been confirmed empirically in tree populations distributed along steep altitudinal clines or across extreme edaphic discontinuities. However, the possibility of microgeographic adaptive divergence due to less severe but more frequent kinds of soil variation is unclear. METHODS: In this study, we looked for evidence of local adaptation to calcareous versus siliceous soil types in two nearby Mediterranean Pinus sylvestris populations connected via pollen flow. Using a greenhouse experiment, we tested for variation in early (up to three years of age) seedling performance among open-pollinated maternal families originating from each edaphic provenance when experimentally grown on both types of natural local substrate. RESULTS: Although seedlings were clearly affected by the edaphic environment, exhibiting lower and slower emergence as well as higher mortality on the calcareous than in the siliceous substrate, neither the performance on each substrate nor the plasticity among substrates varied significantly with seedling edaphic provenance. CONCLUSIONS: We found no evidence of local adaptation to a non-extreme edaphic discontinuity over a small spatial scale, at least during early stages of seedling establishment. Future studies on microgeographic soil-driven adaptation should consider long-term experiments to minimize maternal effects and allow a potentially delayed expression of edaphic adaptive divergence.